Genomics

Sequencher - Sequencher 4.7 (2004) is software for complete DNA sequence analysis for Macintosh and Windows operating systems. Despite its high price (about $2500), Sequencher is powerful and easy to use. It offers several editing options as well as the ability to import many reference sequences from Genbank. (AG)

Datebase management

Access

Microsoft Access - By far the most widely used data base management system in the world.

Strong points:

Very simple to install and does not require complex configuration.

Inter-operability: Since all the data are stored in only one file, it is very simple to distribute a database assembled with Access. This is generally not the case with other systems.

Simplicity in creating forms and applications (with VB).

Weak points:

Does not support "triggers" and procedures.

Reacts badly in environments with several users. Its use should be limited to small databases.

Others

MySQL - Impossible to avoid for people wishing to develop databases using OpenSource software. All documentation as well as the downloadable products can be found on the site. (DL)

Spatial information

Geographic Information Systems

ArcGIS - ArcGIS 9.2 is the new generation of geographic information systems from ESRI (after Arc/INFO and ArcView). By far one of the most complete GIS packages on the market, ArcGIS is an essential research tool in university laboratories and governmental agencies. It is the most widely used GIS software after MapInfo. ArcGIS comes with a module for file management (ArcCatalog), a module for chart editing(ArcMap), a module for geoprocessing (ArcToolBox), a module for 3D visualisation (ArcScene) and a free viewer (ArcReader).

Its strong points are:

File Standards: the shape format (invented by ESRI) is the most widely used vectorial format for geographical information. The new geodatabase format, which replaces the coverage format, offers a much greater possibility of expression for modelling.

Data conversion: ArcGIS includes many very powerful tools for handling geographical objects.

Its weak points are:

Pseudo SQL: Unlike MapInfo, ArcGIS supports only the WHERE function of SQL. It is not possible to make complex requests with GROUP BY, either on several tables or by including only some fields.

Separation of geometrical operations at the editing interface: The tools of geoprocessing are not very well integrated into the chart editing interface (ArcMap).

Its price: The ArcMap module costs approximately $2000 and the complete suite (with the extensions), up to $20,000.

For students at UQAM, the university possesses an institutional license for the ArcGIS suite. For the program to function, your computer (laptop or desktop) must be connected to the UQAM network. To obtain a license, contact Luc Lauzon or Mélanie Desrochers.

Forum ArcGIS - The official forum for ArcGIS support at ESRI. For use in posing the most direct questions. (PR)

Extension and GeoWizards and GeoTools - Two almost-free extensions that simplify conversions of shapefiles from points in lines, from the lines in polygons, and which allow the calculation of areas, perimeters, etc. These extensions can save alot of time!!! However, remember that the free versions are limited in the number of data which they can treat. (SB)

Hawths analysis tools - This extension permits calculations linked to animal locations. It is free and very useful. However, it does not support differences in projections; if you have several shapefiles posted in different projections, you will have to convert them so that they all are visible in a common form. (SB)

Jenness Enterprises - This company has developed a number of extensions for ArcView from its inception and continues to develop others for ArcGis. Almost all these extensions are free and not limited. (SB)

Xtools Pro - This extension is partially free (in its demo version), and gives you access to functionalities not provided by other extensions (go to the site, where they are listed under the Tools pulldown menu). The 30-day test version allows you access to all the functionalities, but afterwards only some functions will remain active. (SB)

ArcView - ArcView 3.2 (1999) and 3.3 (2002) are the much cheaper versions (approximately $2000) of ArcInfo, and comparable to MapInfo. Although ArcView is certainly outmoded by today's standards (e.g., no reprojection on the fly, primitive interface, etc.), it is still used a great deal. Many very useful programs were developed for ArcView with the language Avenue. As ArcGIS no longer supports Avenue, these programs do not necessarily have an equivalent in the latest version and thus will not function.

ArcView is also the name of the basic license for ArcGIS, which is worth about the same price as the older program.

Jenness Enterprises - This company has developed a number of extensions for ArcView from its inception and continues to develope others for ArcGis. Almost all these extensions are free and not limited. (SB)

Others

DNR Garmin - This small program allows you to download Garmin GPS data to a shapefile (ArcGIS) or upload data to the GPS. Garmin DNR user's guide . See chapter 9: Transferring data. (MD)

Tools for correcting French language text

Antidote RX - Antidote Rx(2006), from the Quebec data-processing firm Druide, is the latest update ($69) in the Antidote series. This popular software for correcting French language text continues to capture a greater and greater share of the market. To my knowledge, there is no better program for the task. For a given word, it is possible to search in Antidote for a list of synonyms or antonyms, for phrases containing that word, for analogies, for its anagrams, or for words from the same family. With Antidote you can discover numerous quotations containing that word, together with its complete conjugation, all the while appreciating the intelligent interaction between all these components. With its incomparable richness, its intuitive interface and its amazing speed, Antidote pushes the limits of French dictionaries. Antidote Rx can be installed on both Macintosh PowerPC- and INTEL-based systems, and under Windows and Linux, on machines with 64-bit processors. Attention, Antidote was not created to automatically rewrite your manuscript; rather, it provides you with all of the tools necessary to do a better job in composing text in the first place. (AG)

Statistics

General statistics

R - This powerful program was originally developed by R & R (Ross Ihaka and Robert Gentleman, University of Auckland, New Zealand) as a freeware alternative to S and S-Plus, and ever since its inception has been maintained and refined by a group of volunteer programmers. It's freely downloadable from The R Project, where one can find many other resources.

Its strong points:

Great flexibility in programming that allows the implementation of many statistical analyses and matrix operations

An impressive number of functions for mathematical operations or for less conventional types of analyses is freely available

Freeware

Free upgrades

Several technical books and documents for using the software are available

High quality and flexible graphics

Its weak points:

A good working knowledge of the R language is required to effectively use the program

Absence of a GUI (graphical user interface) for the base version of the program

Tinn-R - This little editor allows you to optimise the use of R, in that it recognises R syntax, provides a possible list of arguments for each function invoked, and makes it possible to directly send script to R (instead of copy and paste into the command window). Note that the editor also recognizes several other languages, including C, C+, C++, HTML, XML, TeX, and JAVA. An indispensable tool for users of R. To avoid having to reconfigure R, I recommend version 1.17.2.4. (MM)

R Graph Gallery - One can find here an assortment of codes necessary for producing a great variety of graphics in R. (MM)

R Site Search - This practical site makes it possible for you to search files in the R-Help list. (MM)

SAS/STAT - This powerful software is the product of SAS Institute. The base module SAS/STAT is devoted to statistical analysis, although several other modules are available for data management and specialised analyses (e.g., ETS for time series and econometric analyses, including simultaneous equation modelling).

Its strong points:

Great flexibility in programming to implement numerous statistical analyses and matrix operations

Macros are available to implement these operations as well as less conventional types of analyses

Several technical books and documents are available regarding the use of this program

Its weak points:

No GUI (graphical user interface)

A good understanding of the SAS language is necessary

High cost of the initial purchase

Cost of the annual license

Cost of updates and additional modules

(Note: many universities pay for an annual license, which enables them to offer SAS free of charge to their research personnel and students)

SAS code taken from SAS books - This site provides numerous data files and code used in a very great number of books that illustrate the use of SAS software. Strongly recommended to whomever wants to reproduce the analyses appearing in SAS publications with the goal of better understanding SAS syntax and its application. (MM)

SAS code and tips from UCLA - This site is rich in SAS code, documents, macros, and practical advice to whomever wishes to optimize their use of SAS/STAT software. (MM)

JMP - This program (John's Macintosh Project, for John Sall, SAS co-founder) is also produced by the SAS Institute, but it is much easier to use than SAS/STAT and is very accessible to the non-corporate user. JMP is more or less SAS with a GUI (graphical user interface) and pull-down menus. This means that the user does not have to learn programming language (although scripting of analyses is possible), but one can rapidly conduct interactive exploratory data analysis (EDA) and graphing on-the-fly -- that is its strength. It is possible to carry out analyses of many kinds, from the very simple (e.g., descriptive statistics, box-plots, etc.) to the very sophisticated (e.g., recursive analysis, partial least-squares regression). JMP is very well suited for the presentation of data and for the export of these results to other software for graphical editing.

JMP is constructed to help users in choosing statistical methods appropriate for their data. This advantage is seldom offered by a statistical analysis software, but can also prove to be a double-edged sword if the user is not familiar with the suggested methods or who does not have access to statistical support. JMP Genomics is a module specialised for the analyses of geomic data.

SPSS tools - One can find many resources here, including an impressive number of tips regarding syntax, macros, and scripts for the users of SPSS. (MM)

Models incorporating the probability of detection

DISTANCE - This software makes it possible to estimate the probability of detection and the abundance of animals starting with data collected under a distance sampling design. It is available free on the site.

Its strong points:

Allows you to estimate abundance after taking the probability of detection into account

Allows you to use particular models when certain assumptions cannot be met (i.e., imperfect detection at distance 0)

Good Windows graphical interface

Note that certain types of analyses, for example, mark-recapture distance sampling, require installation of R, because this analysis is carried out using a library of R functions, after which results are imported into DISTANCE.

MARK - This general-purpose software was developed specifically for a multitude of analyses incorporating the probability of detection for open or closed populations. One can freely download its most recent version from the site, which also includes several technical documents regarding capture-mark-recapture.

Its strong points:

MARK is user-friendly software (with Windows menus), in which one can use menus and sub-menus

MARK supports a great variety of capture-mark-recapture models

You can use design matrices for even greater flexibility

Allows you to simulate data starting with the values of the estimated parameters

Its weak points:

MARK requires large amounts of memory and thus it is necessary to keep the number of open windows in Windows to a minimum; otherwise, the program can become unstable

Requires a good working knowledge of capture-mark-recapture models to avoid errors in modelling

Requires a large screen when one has very large design matrices

MARK Resources on the web

www.phidot.org - One can find several resources on this site, including the excellent of "Program MARK: A gentle introduction ", which should prove to be an indispensable document for whomever wishes to use the MARK program. One can also access a very useful forum for questions regarding capture-mark-recapture analysis. (MM)

PRESENCE - This little program was developed specifically for the site occupancy analyses over one or more seasons. It is freely available from the web site.

Its strong points:

Allows you to model presence/absence analyses, taking into account the probability of detection

Allows you to simulate site occupancy data, using the initial starting values of the parameters

Its weak points:

This software can sometimes be unstable and you are advised to regularly save output

The functionality of Windows is not completely supported by PRESENCE

SURVIV - This extremely, general-purpose software, which is the precursor to MARK, is still being used today for a multitude of capture-mark-recapture analysis. It can be freely downloaded from the site.

Its strong points:

Sa grande flexibilité en fait encore un logiciel utilisé aujourd'hui

Certaines analyses ne peuvent être effectuées qu'avec ce logiciel

Its weak points:

DOS and FORTRAN environment

A very good understanding of programming and the theory behind capture-mark-recapture models is necessary

Not advised for neophytes to the subject

Other sites where one can obtain software incorporating the probability of détection

Patuxent Software Archive - From this site, one can download a variety of software, many which were developed by Jim Hines of the Patuxent Wildlife Research Center, that allow you to estimate of the probability of detection rising from capture-mark-recapture techniques. (MM)

CNRS Montpellier - From this site, one can download capture-mark-recapture software (M-SURGE) as well as software that allows you to test the goodness-of-fit of survival and multi-stage models. (MM)

Interested users should note that versions prior to 4.5 are not very flexible with respect to data importation from other programs and that graphical presentation with Canodraw is very limited.

ADE-4 is software developed by the Laboratory of Biometrics and Evolutionary Biology at the University of Lyon. It contains functions for the Analysis of Data that include both Ecological and Environmental measurements, which can be Explored through Euclidean-based procedures; hence, the acronym ade-4.

Since 2004, this freeware has been available under R for Mac, Windows, Linux and Unix systems. The old, non-R version of the software (ADE-4) for Windows and Mac is also available here, but it has not been maintained since 2004. (BP)

Marti Jane Anderson has created a set of multivariate freeware executables for Windows and the Mac. At the core of each program is a permutation test, for the Canonical Analysis of Principal Coordinates (Program CAP, also does Canonical Correlation and Canonical Discriminant Function Analyses), MANOVA (Programs PERMANOVA and DISTLM), MANCOVA (DISTLM), and multivariate multiple regression (DISTLM and DISTLM_forward, the latter is for stepwise regression). The accompanying program XMATRIX allows you to construct the design matrix for the overall ANOVA or regression model, together with matrices for specific tests of main effects, interactions and contrasts -- I prefer to create these myself as text files in EXCEL.

When calculating similarities among samples, you have a large selection of indices from which to choose, or the option of using euclidean distance. The programs are ideally used with data sets that contain many variables and few cases (she includes Program PCO, a permutation-based program for obtaining a principal coordinates solution), and for data that are not likely to conform to either multivariate or univariate assumptions of normality and homogeneity of variance among treatments. With respect to the latter assumption, she has written programs for evaluating multivariate homoskedasticity using PERMDISP and PERMDISP2 (multivariate extensions of Levene's test).
(BP)

Blossom – Freeware allowing to build quantile regression models with accompanying permutation tests of significance, by Brian Cade and Jon Richards, US Geological Survey, Fort Collins, Colorado. Blossom can also perform MRPP (Multiresponse Permutation Procedure) tests; hence its inclusion under multivariate statistical methods. A number of other programs produced by the USGS can be downloaded from this site.